Home







      Zhiye Tang

        Active Job Seeker

        Postdoctoral Researcher at University of California, Riverside

        To CV Page (EN & JP)







Summary

Ph.D. with broad and deep knowledge in chemical and biological processes, necessary mathematics and physics; Expertise in modeling binding processes and their thermodynamics and kinetics; Adept at applying and developing methods that solve problems in categories of non-bonding interaction and biological processes; acknowledged by supervisors and colleagues for professionalism, commitment to excellence, demonstrated ability to communicate and collaborate, and well prepared mentorship for the juniors; able to handle multiple projects; productive even under pressure; self-motivated and experienced in both independent and collaborative projects; outstanding in scientific presentations and good in scientific writings.





Experiences


University of California, Riverside

Postdoctoral Researcher                                                                                                              Sept 2016-Present

Graduate Research Assistant                                                                                                       Sept 2011-Aug 2016


Research theme: 

        Modeling Molecular Recognition from Thermodynamics to Kinetics: 

        Affinity, Selectivity, Binding Rates and Binding Pathways

Projects:

1. Novel Dissociation Pathway Search Method Inspired by Principal Component Analysis

2. Thermodynamics and Kinetics Calculations of β-Cyclodextrin and Guest Binding Process

3. Study of CDK8-Ligand Binding Affinities and Dissociation Pathways

4. Explanation of Selective Binding of Various Surfactants on Silver nano-Plate Facets

5. Study of Inhibitor MitoBloCK-10 Resistance on TIM44 Protein and Its Mutants

6. Catalytic Efficiency of Salmonella Tryptophan Synthase (TRPS) and Its Homologue BX1 in Maize




Education


  Ph.D. in Chemistry

  University of California, Riverside                             

  September 2011-August 2016

 

  Bachelor of Science in Chemistry

  Wuhan University                    

  September 2007-June 2011






Publications


Facet Selectivity of Ligands on Silver Nanoplates: Molecular Mechanics Study

Journal of Physical Chemistry C, 2014

Systematic Dissociation Pathway Searches Guided by Principal Component Modes

Journal of Chemical Theory and Computation, 2017

Understanding Ligand-Receptor Non-Covalent Binding Kinetics Using Molecular Modeling

Frontiers in Bioscience, 2016

Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition

(Submitted)

Energy Barriers, Molecular Motions, and Residence Time in Ligand Dissociation: A Computational Study on Type II Inhibitors Binding to CDK8/CycC

(Submitted)

A Molecular Dynamics Investigation of CDK8/CycC and Ligand Binding: Conformational Flexibility and Implication in Drug Discovery

(Submitted)

Adaptation of a Genetic Screen Reveals an Inhibitor for Mitochondrial Protein Import Component Tim44

The Journal of Biological Chemistry, 2017

A QM/MM Study of Biomimetic Catalysis of Diels-Adler Reactions Using Cyclodextrins

(Submitted)

Evaluating the Accuracy of the Umbrella Sampling Plots with Different Dissociation Paths, Conformational Changes, and Structure Preparation

(Submitted)





Computer Based Skills


Computational and Modeling Software: 

Molecular/Brownian Dynamics:

AMBER, NAMD, Metadynamics, GaMD, GeomBD, NAM

Conformational Search/Docking:

Autodock, Autodock Vina, VDock, Mining Minima 2

Protonation State Determination:

MCCE, ProPKa, DelPhiPKa

Free Energy Calculation:

Umbrella Sampling (WHAM), Milestoning 

Visualization and Modeling:

Vega ZZ, Avogadro, VMD, PyMol 

Database:

Cambridge Crystallographic Data Centre, PDB Data Bank, Pfam 

Others:

In House Packages, Personal Analysis Library and Tools 

Programming Languages: 

Proficient:

C++, VC, Fortran, Basic, Mathematica, Direct X, Intel MKL Library 

Sufficient:

PERL, PYTHON, R, Cuda 

General Software:

Microsoft Office, 3DS MAX, PHOTOSHOP




Languages






English                                          Full Professional Proficiency 


Chinese                                        Native 


Japanese                                      Full Conventional Proficiency/Professional Sufficiency



Last update: Sept 1, 2017